Variant report

Variant	rs2057138
Chromosome Location	chr14:39943868-39943869
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr14:39943765-39943915	HepG2	liver:	n/a	n/a
2	SMC3	chr14:39943843-39944039	HepG2	liver:	n/a	n/a
3	SPI1	chr14:39943553-39943886	GM12891	blood:	n/a	n/a
4	RELA	chr14:39943706-39944199	GM19193	blood:	n/a	n/a
5	NFIC	chr14:39943506-39944361	GM12878	blood:	n/a	n/a
6	HNF4A	chr14:39943692-39944131	HepG2	liver:	n/a	chr14:39943948-39943963
7	HNF4A	chr14:39943768-39944167	HepG2	liver:	n/a	chr14:39943948-39943963
8	RUNX3	chr14:39943571-39944252	GM12878	blood:	n/a	n/a
9	ARID3A	chr14:39943811-39944146	HepG2	liver:	n/a	n/a
10	MAFF	chr14:39943664-39944019	HepG2	liver:	n/a	chr14:39943852-39943870
11	JUN	chr14:39943854-39944169	HepG2	liver:	n/a	chr14:39944002-39944015
12	RUNX3	chr14:39943617-39944197	GM12878	blood:	n/a	n/a
13	MAFK	chr14:39943713-39944035	HepG2	liver:	n/a	n/a
14	ATF2	chr14:39943665-39944235	GM12878	blood:	n/a	n/a
15	MAX	chr14:39943797-39944062	HepG2	liver:	n/a	n/a
16	SPI1	chr14:39943602-39943981	GM12891	blood:	n/a	n/a
17	MAFK	chr14:39943683-39944029	HepG2	liver:	n/a	n/a
18	SPI1	chr14:39943573-39943893	GM12878	blood:	n/a	n/a
19	IRF4	chr14:39943761-39944180	GM12878	blood:	n/a	n/a
20	PAX5	chr14:39943691-39944182	GM12878	blood:	n/a	n/a
21	WRNIP1	chr14:39943799-39943870	GM12878	blood:	n/a	n/a
22	RELA	chr14:39943713-39944188	GM18951	blood:	n/a	n/a
23	TBP	chr14:39943639-39943939	GM12878	blood:	n/a	n/a
24	EP300	chr14:39943704-39944169	GM12878	blood:	n/a	chr14:39943782-39943795
25	NFIC	chr14:39943605-39944221	GM12878	blood:	n/a	n/a
26	CEBPB	chr14:39943715-39944279	GM12878	blood:	n/a	n/a
27	FOXM1	chr14:39943662-39944253	GM12878	blood:	n/a	n/a
28	BCL11A	chr14:39943701-39944122	GM12878	blood:	n/a	n/a
29	HNF4G	chr14:39943742-39944181	HepG2	liver:	n/a	chr14:39943949-39943964
30	HNF4A	chr14:39943780-39944114	HepG2	liver:	n/a	chr14:39943948-39943963
31	MTA3	chr14:39943710-39944147	GM12878	blood:	n/a	n/a
32	JUND	chr14:39943843-39944179	HepG2	liver:	n/a	n/a
33	CHD2	chr14:39943786-39944120	HepG2	liver:	n/a	n/a
34	PML	chr14:39943667-39944272	GM12878	blood:	n/a	n/a
35	ATF2	chr14:39943728-39944148	GM12878	blood:	n/a	n/a
36	MAZ	chr14:39943826-39944040	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTAGE5-1	chr14:39943747-39944159	NONHSAT036542

Variant related genes	Relation type
ENSG00000258526	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10137905	0.82[CHB][hapmap]
rs11157067	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11847057	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12587625	0.95[AFR][1000 genomes]
rs12588110	0.95[AFR][1000 genomes]
rs12588175	0.93[AFR][1000 genomes]
rs12588483	0.96[AFR][1000 genomes]
rs12589427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12590172	0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12880644	0.95[AFR][1000 genomes]
rs12884747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12886696	0.82[ASN][1000 genomes]
rs12886769	0.89[AFR][1000 genomes]
rs12894147	0.97[ASN][1000 genomes]
rs12894855	0.83[CHB][hapmap]
rs12896502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1304254	0.84[ASN][1000 genomes]
rs17109296	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs17109300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109328	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1807940	0.82[ASN][1000 genomes]
rs1950329	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1950330	0.82[ASN][1000 genomes]
rs1950331	0.82[ASN][1000 genomes]
rs1950333	0.82[ASN][1000 genomes]
rs1950334	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1950335	0.82[ASN][1000 genomes]
rs1950336	0.98[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1950338	0.97[AFR][1000 genomes]
rs1955718	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1955726	0.82[ASN][1000 genomes]
rs1955729	0.84[CHB][hapmap];0.96[JPT][hapmap];0.82[ASN][1000 genomes]
rs2057137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2057139	0.94[ASN][1000 genomes]
rs2207291	0.97[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2207293	0.82[ASN][1000 genomes]
rs2274395	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2274396	0.82[CHB][hapmap]
rs2415549	0.95[AFR][1000 genomes]
rs2415550	0.98[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2899889	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34432449	0.95[ASN][1000 genomes]
rs34649642	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34687394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35459433	0.95[AFR][1000 genomes]
rs35553183	0.95[AFR][1000 genomes]
rs35643160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35693868	0.93[AFR][1000 genomes]
rs35708308	0.84[ASN][1000 genomes]
rs35923045	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36010374	0.98[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3814860	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4899277	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4899278	0.99[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4899287	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899291	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902569	0.82[CHB][hapmap]
rs4902570	0.82[CHB][hapmap]
rs4902622	0.91[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4902636	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4902637	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4902648	0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4902665	0.95[AFR][1000 genomes]
rs4902676	0.97[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4902692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56046902	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs71407788	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs71407789	0.97[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7140983	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7152341	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7152935	0.97[AFR][1000 genomes]
rs7158709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7161403	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs719455	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs72675487	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8003397	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8003621	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8006123	0.95[AFR][1000 genomes]
rs8006321	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs8020250	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs910370	0.92[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs910371	0.97[AFR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv832774	chr14:39897746-40060823	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39939000-39946000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr14:39939000-39954600	Weak transcription	Brain Hippocampus Middle	brain
3	chr14:39941000-39944200	Weak transcription	Fetal Heart	heart
4	chr14:39943400-39944400	Enhancers	GM12878-XiMat	blood
5	chr14:39943400-39944400	Enhancers	HepG2	liver

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